Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.55 kDa 
• Atom Count: 2608 
• Residue Count: 302 
• Unique protein chains: 2

1TGZ

Structure of human Senp2 in complex with SUMO-1

• DOI: 10.2210/pdb1TGZ/pdb

• Classification: CELL CYCLE, HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-05-31 Released: 2004-09-14 
• Deposition Author(s): Reverter, D., Lima, C.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.276 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex

Reverter, D., Lima, C.D.

(2004) Structure 12: 1519-1531

• PubMed: 15296745 
• DOI: 10.1016/j.str.2004.05.023
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Modification of cellular proteins by the ubiquitin-like protein SUMO is essential for nuclear metabolism and cell cycle progression in yeast. X-ray structures of the human Senp2 catalytic protease domain and of a covalent thiohemiacetal transition-state complex obtained between the Senp2 catalytic domain and SUMO-1 revealed details of the respective protease and substrate surfaces utilized in interactions between these two proteins. Comparative biochemical and structural analysis between Senp2 and the yeast SUMO protease Ulp1 revealed differential abilities to process SUMO-1, SUMO-2, and SUMO-3 in maturation and deconjugation reactions. Further biochemical characterization of the three SUMO isoforms into which an additional Gly-Gly di-peptide was inserted, or whereby the respective SUMO tails from the three isoforms were swapped, suggests a strict dependence for SUMO isopeptidase activity on residues C-terminal to the conserved Gly-Gly motif and preferred cleavage site for SUMO proteases.

---

Organizational Affiliation: 

Structural Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Sentrin-specific protease 2	A	226	Homo sapiens	Mutation(s): 0  Gene Names: SENP2, KIAA1331 EC: 3.4.22
Find proteins for Q9HC62 (Homo sapiens) Explore Q9HC62  Go to UniProtKB:  Q9HC62
NIH Common Fund Data Resources
PHAROS  Q9HC62 GTEx  ENSG00000163904

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-like protein SMT3C	B	80	Homo sapiens	Mutation(s): 0  Gene Names: UBL1, SMT3H3, SMT3C, SUMO1, OK/SW-cl.43
Find proteins for P63165 (Homo sapiens) Explore P63165  Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS  P63165 GTEx  ENSG00000116030

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.276 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.163	α = 90
b = 111.163	β = 90
c = 143.106	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-31 
• Released Date: 2004-09-14 
Deposition Author(s): Reverter, D., Lima, C.D.

Revision History 

• Version 1.0: 2004-09-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance